ESM 244 Lab 9 Key

Today:

• Some network graphs
• Sankey diagrams
• Datapasta
• Nice tables with gt
• A code alarm clock
• Some other useful things

library(beepr) # beep (on CRAN)
library(datapasta) # copy/paste (on CRAN)
library(tidyverse) 
library(igraph) # network stuff (on CRAN)
library(multiplex) # network stuff (on CRAN)
library(ggraph) # More graph stuff (on CRAN)
library(gt) # tables (get development version!!!)
# remotes::install_github("rstudio/gt")
library(ggalluvial) # Sankeys (on CRAN)
library(readxl) # Get .xls (on CRAN)
library(praise) # Get/share praise! 

# Note: may need to update dependencies (I usually choose yes to all...)

Part 1. Network analysis example (Les Miserables character connections)

Get the data

# Stored as a .gml file (graph modeling language) format supports network data
# Use multiplex::read.gml()

lm_df <- read.gml("lesmis.gml")

# Convert to graph (igraph) with nodes & edges
les_mis <- graph_from_data_frame(lm_df, directed = FALSE)
beep(sound = 2)

Find some quantitative metrics:

#Graph diameter:
diameter(les_mis) # Smallest maximum distance (links)

## [1] 5

# Farthest vertices
farthest_vertices(les_mis)

## $vertices
## + 2/77 vertices, named, from 4e68f8b:
## [1] Napoleon  Jondrette
## 
## $distance
## [1] 5

Plot it:

# Alternatively, get the graph data as igraph right away with igraph::read_graph()
# les_mis <- read_graph("lesmis.gml", format = "gml")

plot(les_mis,
     vertex.color = "orange",
     vertex.frame.color = "NA",
     vertex.size = 5,
     vertex.label.color = "black",
     vertex.label.cex = 0.5,
     vertex.label.dist = 2)

Other graphing options: ggraph ggnet2 plot + more…

A really cool resource for network plots in ggraph: https://www.data-imaginist.com/2017/ggraph-introduction-layouts/

Want to do it more in the style of ggplot? Use ggraph.

# Then plot it
ggraph(les_mis, layout = 'kk') +
  geom_edge_link() +
  geom_node_text(aes(label = name), size = 2, color = "white") +
  theme_dark()

# Or an arc graph: 
ggraph(les_mis, layout = "linear") + 
  geom_edge_arc(alpha = 0.8) + 
  geom_node_text(aes(label = name), angle = 90, size = 2, hjust = 1) +
  theme_graph()

# Try layout = "circle", "tree"
ggraph(les_mis, layout = "tree") +
  geom_edge_fan(color = "gray90") + 
  geom_node_text(aes(label = name), size = 2, color = "black", angle = 45) +
  theme_void()

One like the layouts you’re probably most used to seeing:

# And a circular form of linear arcs:

ggraph(les_mis, layout = "linear", circular = TRUE) +
  geom_edge_arc(alpha = 0.5) +
  geom_node_point(aes(colour = name), show.legend = FALSE) +
  geom_node_text(aes(label = name), size = 3, hjust = "outward") +
  theme_void()

Part 2. Sankey diagrams showing flows

Note: there are other options for creating Sankey diagrams. Other packages to look into for Sankeys: alluvial, ggalluvial, NetworkD3

Wikipedia: “Sankey diagrams are a specific type of flow diagram, in which the width of the arrows is shown proportionally to the flow quantity.”

Let’s just get some simple data that I’ve created:

sdf <- read_csv("sankey_df.csv") %>% 
  select(-X1)

## Warning: Missing column names filled in: 'X1' [1]

## Parsed with column specification:
## cols(
##   X1 = col_integer(),
##   before = col_character(),
##   after = col_character(),
##   weight = col_integer()
## )

# OK, now I want to make a diagram of those flows...

Then plot it with ggalluvial: A cool resource: https://matthewdharris.com/2017/11/11/a-brief-diversion-into-static-alluvial-sankey-diagrams-in-r/

ggplot(sdf, aes(y = weight, axis1 = before, axis2 = after)) +
  geom_alluvium(aes(fill = before, color = before), show.legend = FALSE, width = 1/5) +
  geom_stratum(width = 1/5, color = "gray") +
  geom_text(stat = "stratum", label.strata = TRUE) +
  scale_fill_manual(values = c("purple","blue","green")) +
  scale_color_manual(values = c("purple","blue","green")) +
  scale_x_discrete(limits = c("Before", "After"), expand = c(0,0)) +
  theme_minimal()

## Warning in to_lodes_form(data = data, axes = axis_ind, discern =
## params$discern): Some strata appear at multiple axes.

## Warning in to_lodes_form(data = data, axes = axis_ind, discern =
## params$discern): Some strata appear at multiple axes.

## Warning in to_lodes_form(data = data, axes = axis_ind, discern =
## params$discern): Some strata appear at multiple axes.

Part 3. A few of my favorite things right now

3a. Let’s make our own tibble!

A tibble is like a data frame with a little more functionality. From r4ds: “Tibbles are data frames, but they tweak some older behaviours to make life a little easier.” Tibble and data frame are mostly used interchangeably.

my_tibble <- tribble(
  ~allison, ~made, ~this, ~table,
  1,"yes",0,10000,
  2,"no",10, 20000,
  3,"maybe",20, 5000,
  4,"yes",15, 12000,
  5,"no",25, 18000
)

# Then it just works like anything else...
ggplot(my_tibble, aes(x = allison, y = table)) +
  geom_point(aes(color = made), size = 10) +
  scale_color_manual(values = c("red","orange","yellow")) +
  theme_dark()

3b. But now, datapasta!

Cool, so I can make my own data frames (tibbles) right here in R in a really intuitive way. But a lot of times there’s data somewhere that we want in R, but it doesn’t exist in a super useful format online. That’s annoying. Luckily for us, there’s datapasta!

datapasta from Miles McBain: https://github.com/MilesMcBain/datapasta

Once you install datapasta, then you should be able to find the datapasta addin (Tools > Addins > datapasta paste as tribble).

Go to page on “How to datapasta:” https://cran.r-project.org/web/packages/datapasta/vignettes/how-to-datapasta.html

• copy table to clipboard
• go to Tools -> Addins -> datapasta:: paste as tribble

• ta da!

• Want it to be even easier to use? Create a keyboard shortcut for addins! (mine is shift + command + t)…they might want to see how to create those R shortcuts?

weather_data <- tibble::tribble(
                                ~X,          ~Location, ~Min, ~Max,
                  "Partly cloudy.",         "Brisbane",  19L,  29L,
                  "Partly cloudy.", "Brisbane Airport",  18L,  27L,
                "Possible shower.",       "Beaudesert",  15L,  30L,
                  "Partly cloudy.",        "Chermside",  17L,  29L,
  "Shower or two. Possible storm.",           "Gatton",  15L,  32L,
                "Possible shower.",          "Ipswich",  15L,  30L,
                  "Partly cloudy.",    "Logan Central",  18L,  29L,
                   "Mostly sunny.",            "Manly",  20L,  26L,
                  "Partly cloudy.",    "Mount Gravatt",  17L,  28L,
                "Possible shower.",            "Oxley",  17L,  30L,
                  "Partly cloudy.",        "Redcliffe",  19L,  27L
  )

weather_data <- rename(weather_data, Condition = X)

You can also do this from things like an Excel file. Open the PesticideResidues.xls file on your computer. Select a subset of the cells (don’t include headers for this example). Then use datapasta to create a tibble from it in R (remember, my shortcut is Control + Shift + t):

pest_sub <- tibble::tribble(
          ~V1,                           ~V2,      ~V3,          ~V4,           ~V5,
  "06-Jan-14",                        "KALE", 2140001L, "California",   "Riverside",
  "06-Jan-14",                        "KALE", 2140001L, "California",   "Riverside",
  "06-Jan-14",                        "KALE", 2140001L, "California",   "Riverside",
  "06-Jan-14",  "STRAWBERRY (ALL OR UNSPEC)", 2140002L, "California", "Santa Maria",
  "06-Jan-14",  "STRAWBERRY (ALL OR UNSPEC)", 2140002L, "California", "Santa Maria",
  "06-Jan-14",  "STRAWBERRY (ALL OR UNSPEC)", 2140002L, "California", "Santa Maria",
  "06-Jan-14",  "STRAWBERRY (ALL OR UNSPEC)", 2140002L, "California", "Santa Maria",
  "06-Jan-14",  "STRAWBERRY (ALL OR UNSPEC)", 2140002L, "California", "Santa Maria",
  "06-Jan-14",      "ORANGE (ALL OR UNSPEC)", 2140003L, "California",       "Arvin",
  "06-Jan-14",      "ORANGE (ALL OR UNSPEC)", 2140003L, "California",       "Arvin",
  "06-Jan-14",      "ORANGE (ALL OR UNSPEC)", 2140003L, "California",       "Arvin",
  "06-Jan-14", "PEAR, ASIAN (ORIENTAL PEAR)", 2140004L, "California",   "Kingsburg",
  "06-Jan-14", "PEAR, ASIAN (ORIENTAL PEAR)", 2140004L, "California",   "Kingsburg",
  "06-Jan-14", "PEAR, ASIAN (ORIENTAL PEAR)", 2140004L, "California",   "Kingsburg",
  "06-Jan-14",                     "SPINACH", 2140005L, "California",    "Highland",
  "06-Jan-14",                     "SPINACH", 2140005L, "California",    "Highland",
  "06-Jan-14",                     "SPINACH", 2140005L, "California",    "Highland"
  )

3c. Beautiful tables with gt

The gt package by Rich Iannone is awesome (https://github.com/rstudio/gt).

Cool, so gt just works…

weather_data %>% 
  gt()

Condition	Location	Min	Max
Partly cloudy.	Brisbane	19	29
Partly cloudy.	Brisbane Airport	18	27
Possible shower.	Beaudesert	15	30
Partly cloudy.	Chermside	17	29
Shower or two. Possible storm.	Gatton	15	32
Possible shower.	Ipswich	15	30
Partly cloudy.	Logan Central	18	29
Mostly sunny.	Manly	20	26
Partly cloudy.	Mount Gravatt	17	28
Possible shower.	Oxley	17	30
Partly cloudy.	Redcliffe	19	27

Or make it way better:

https://gt.rstudio.com/reference/tab_options.html

weather_data %>% 
  gt() %>% 
  tab_header(
    title = "An amazing title", # Add a title
    subtitle = "(by Allison!)"# And a subtitle
  ) %>%
  fmt_passthrough( # Not sure about this but it works...
    columns = vars(Location) # First column: supp (character)
  ) %>% 
  fmt_number(
    columns = vars(Min), # Second column: mean_len (numeric)
    decimals = 1 # With 4 decimal places
  ) %>% 
    fmt_number(
    columns = vars(Max), # Third column: dose (numeric)
    decimals = 1 # With 2 decimal places
  ) %>% 
  cols_move_to_start(
    columns = vars(Location)
  ) %>% 
  data_color( # Update cell colors...
    columns = vars(Min), # ...for mean_len column
    colors = scales::col_numeric(
      palette = c(
        "darkblue", "blue"), # Overboard colors! 
      domain = c(20,14) # Column scale endpoints
  )
  ) %>% 
  data_color(
    columns = vars(Max),
    colors = scales::col_numeric(
      palette = c(
       "yellow", "orange", "red"),
      domain = c(26,32)
      )
    ) %>% 
  tab_options(
    table.background.color = "purple",
    heading.background.color = "black",
    column_labels.background.color = "gray",
    heading.border.bottom.color = "yellow",
    column_labels.font.size = 10
  )

An amazing title
(by Allison!)
Location	Condition	Min	Max
Brisbane	Partly cloudy.	19.0	29.0
Brisbane Airport	Partly cloudy.	18.0	27.0
Beaudesert	Possible shower.	15.0	30.0
Chermside	Partly cloudy.	17.0	29.0
Gatton	Shower or two. Possible storm.	15.0	32.0
Ipswich	Possible shower.	15.0	30.0
Logan Central	Partly cloudy.	18.0	29.0
Manly	Mostly sunny.	20.0	26.0
Mount Gravatt	Partly cloudy.	17.0	28.0
Oxley	Possible shower.	17.0	30.0
Redcliffe	Partly cloudy.	19.0	27.0

# And see https://gt.rstudio.com/reference/tab_options.html for mor overall formatting!

See more examples here: https://github.com/allisonhorst/gt-awesome-tables

3d. Reading in straight from a URL

Google then direct to get to the UCI Machine Learning data for auto-mpg. Then read it in via the URL. Make sure to ask yourself: why is this convenient but risky?

• Google: U.S. Nuclear Power Reactor Plant Status
• From: data.gov
• Then click on ‘text file’ under Downloads and Resources
• Copy URL

Note: don’t want to have reading from URL in document that’s knitting (requires connection)…? Depends.

# nuclear <- read_delim("https://www.nrc.gov/reading-rm/doc-collections/event-status/reactor-status/PowerReactorStatusForLast365Days.txt", delim = "|", col_names = TRUE)

# Because you always want a version of what you were working with, I recommend writing that to a csv (or a text file, or whatever)

# write_csv(nuclear, "nuclear.csv")

But that also works if it’s in your working directory…

3e. Reading in Excel files (and skipping top rows metadata)

Easy to read in Excel files (respecting the classes):

pesticides <- read_xls("PesticideResidues.xls")

## New names:
## * `` -> `..2`
## * `` -> `..3`
## * `` -> `..4`
## * `` -> `..5`
## * `` -> `..6`
## * … and 11 more

# Dang, there are two extra rows with information in them. Bummer. But: 

pest2 <- read_xls("PesticideResidues.xls", skip = 2, col_names = TRUE) # Ta da! 

pest <- pest2 %>% 
  janitor::clean_names()

Let’s clean that up, do some wrangling, and a cool visualization to close out 244 lab for the year

Some wrangling of the pesticide data:

crops <- pest %>% 
  filter(commodity == "KALE",!is.na(grower_city)) %>% 
  separate(grower_city, c("grow_city","grow_state"), sep = ",") %>% 
  separate(collection_site_city, c("market_city","market_state"), sep = ",") %>% 
  group_by(organic_commodity, grow_city, market_city) %>% 
  tally()

## Warning: Expected 2 pieces. Missing pieces filled with `NA` in 93 rows
## [1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32,
## 33, ...].

## Warning: Expected 2 pieces. Missing pieces filled with `NA` in 93 rows
## [1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32,
## 33, ...].

Then a Sankey diagram!

ggplot(crops, aes(y = n, axis1 = organic_commodity, axis2 = grow_city, axis3 = market_city)) +
  geom_alluvium(aes(fill = organic_commodity, color = organic_commodity), show.legend = FALSE, width = 1/5) +
  geom_stratum(width = 1/5, color = "gray") +
  geom_text(stat = "stratum", label.strata = TRUE, size = 2) +
  scale_fill_manual(values = c("purple","blue")) +
  scale_color_manual(values = c("purple","blue")) +
  scale_x_discrete(limits = c("status", "grown","market"), expand = c(0,0)) +
  scale_y_continuous(expand = c(0,0)) +
  theme_bw()

## Warning in to_lodes_form(data = data, axes = axis_ind, discern =
## params$discern): Some strata appear at multiple axes.

## Warning in to_lodes_form(data = data, axes = axis_ind, discern =
## params$discern): Some strata appear at multiple axes.

## Warning in to_lodes_form(data = data, axes = axis_ind, discern =
## params$discern): Some strata appear at multiple axes.

Other things to show during this lab:

• Comment out multiple lines with Command + Shift + c
• Selecting a whole line or parts: Command + Shift + arrow
• Just shift arrow for by letter